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- PDB-1z7f: Crystal structure of 16 base pair RNA duplex containing a C-A mismatch -

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Basic information

Entry
Database: PDB / ID: 1z7f
TitleCrystal structure of 16 base pair RNA duplex containing a C-A mismatch
Components5'-R(*GP*CP*AP*GP*AP*CP*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3'
KeywordsRNA / DUPLEX / MISMATCH
Function / homologySTRONTIUM ION / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGherghe, C.M. / Krahn, J.M. / Weeks, K.M.
CitationJournal: J.Am.Chem.Soc. / Year: 2005
Title: Crystal structures, reactivity and inferred acylation transition States for 2'-amine substituted RNA.
Authors: Gherghe, C.M. / Krahn, J.M. / Weeks, K.M.
History
DepositionMar 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-R(*GP*CP*AP*GP*AP*CP*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3'
B: 5'-R(*GP*CP*AP*GP*AP*CP*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3'
C: 5'-R(*GP*CP*AP*GP*AP*CP*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4215
Polymers15,2463
Non-polymers1752
Water1,20767
1
A: 5'-R(*GP*CP*AP*GP*AP*CP*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3'
hetero molecules

A: 5'-R(*GP*CP*AP*GP*AP*CP*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3394
Polymers10,1642
Non-polymers1752
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
2
B: 5'-R(*GP*CP*AP*GP*AP*CP*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3'
C: 5'-R(*GP*CP*AP*GP*AP*CP*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2523
Polymers10,1642
Non-polymers881
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.000, 43.000, 122.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-17-

SR

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Components

#1: RNA chain 5'-R(*GP*CP*AP*GP*AP*CP*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3'


Mass: 5082.079 Da / Num. of mol.: 3 / Source method: obtained synthetically
#2: Chemical ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Sr
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 7
Details: MPD, sodium cacodylate, spermine, strontium chloride, magnesium chloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 273K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2sodium cacodylate11
3spermine11
4strontium chloride11
5magnesium chloride11
6H2O11
7MPD12
8sodium cacodylate12
9strontium chloride12
10magnesium chloride12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Feb 14, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→27 Å / Num. all: 9573 / Num. obs: 8972 / % possible obs: 93.8 % / Observed criterion σ(I): 1 / Redundancy: 12.02 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.108 / Net I/σ(I): 22.11
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 4.59 / Num. unique all: 638 / Rsym value: 0.158 / % possible all: 68.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1YRM

1yrm


Resolution: 2.1→19.01 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1006060.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.28 448 5.7 %RANDOM
Rwork0.261 ---
all0.275 ---
obs0.261 7927 97.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.0469 Å2 / ksol: 0.353048 e/Å3
Displacement parametersBiso mean: 33.4 Å2
Baniso -1Baniso -2Baniso -3
1-4.87 Å23.33 Å20 Å2
2--4.87 Å20 Å2
3----9.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1008 2 67 1077
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d6.3
X-RAY DIFFRACTIONc_improper_angle_d1.34
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scbond_it1.592
X-RAY DIFFRACTIONc_scangle_it2.032.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.328 71 5.8 %
Rwork0.299 1163 -
obs--93 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION2DNA-RNA.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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